this might be a simple question however I could not find any answers after googling, reading some documentations and descriptions.

Basically I have around a 100 tigram domains and then I augmented some domains that were not found in tigrfam database from pfam DB such as Ribosomal S9 domain.

I want to compile a database of these tigrfams and pfams to one file database, what I did is I concatenated the flat files from pfam and tigrfam into one file and then tried to issue an hmmpress command to compress and create the binaries for the database and the program is complaining

Working... bad file format in HMM file pfam_tigrfam_abundant.hmm

I think this is due to the fact im mixing hmm domains from both databases, if I issue hmmpress on the two sets separately it is working just fine.

Does anyone know how I can compile a single database file? Maybe convert pfams into tigrfams somehow? Thanks for your time.

Concatenating HMM text files should not cause any issues, and mixing databases shouldn't either. hmmpress has no concept of database affiliations. I would check whether all your HMMs were made by the same HMMer version - it is listed in the very first line of each HMM.

My recent Pfam HMMs have this line:

HMMER3/f [3.1b2 | February 2015]

TIGRFAM HMMs that I have (v15):

HMMER3/b [3.0 | March 2010]

Converting TIGRFAM HMMs into the same format as your hmmpress should do the trick. See here.